In Freud's defense, it does seem like a universal truth that people want more. When our neighbor has more stuff, we envy him. We hoard stuff, even when we don't use them.
A second apparently universal principle is that humans are very visual creatures. It's probably our most important sense, both subjectively and perhaps objectively.
Putting these two together, the idea of penis envy becomes 'intuitively appealing', because visually we can't see what's inside, the dangling thing is more attention-grabbing, and people just tend to want more of everything.
Perhaps, also, if girls notice a difference in treatment from that age, favoring boys, and the only difference they can observe visually at that prepubescent age is the penis, then they might attribute said differential treatment to the penis, and therefore begin to envy it. 🤷♂️